Starting phenix.real_space_refine on Tue Dec 12 15:45:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/12_2023/8gka_40181_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/12_2023/8gka_40181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/12_2023/8gka_40181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/12_2023/8gka_40181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/12_2023/8gka_40181_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/12_2023/8gka_40181_updated.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 14361 2.51 5 N 3409 2.21 5 O 3884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 354 Unusual residues: {' NA': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 435 Unusual residues: {'POV': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 291 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 10.93, per 1000 atoms: 0.50 Number of scatterers: 21812 At special positions: 0 Unit cell: (164.628, 164.628, 129.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 33 15.00 Na 1 11.00 O 3884 8.00 N 3409 7.00 C 14361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.42 Conformation dependent library (CDL) restraints added in 3.6 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 56.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.586A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 Processing helix chain 'A' and resid 484 through 508 Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.694A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 685 removed outlier: 3.898A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.587A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 Processing helix chain 'B' and resid 484 through 508 Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 3.693A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.897A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.587A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 Processing helix chain 'C' and resid 484 through 508 Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 3.694A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 685 removed outlier: 3.898A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.587A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 Processing helix chain 'D' and resid 484 through 508 Processing helix chain 'D' and resid 513 through 519 Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 566 removed outlier: 3.694A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 685 removed outlier: 3.898A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 376 through 382 removed outlier: 3.546A pdb=" N ASP A 379 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS A 731 " --> pdb=" O GLY A 718 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY A 718 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP B 379 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 731 " --> pdb=" O GLY B 718 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY B 718 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP C 379 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS C 731 " --> pdb=" O GLY C 718 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY C 718 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 382 removed outlier: 3.548A pdb=" N ASP D 379 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS D 731 " --> pdb=" O GLY D 718 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY D 718 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.45: 5647 1.45 - 1.57: 12727 1.57 - 1.69: 66 1.69 - 1.81: 204 Bond restraints: 22222 Sorted by residual: bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.77e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.69e-02 3.50e+03 5.38e-01 bond pdb=" CB PRO C 510 " pdb=" CG PRO C 510 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.36e-01 ... (remaining 22217 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.16: 248 104.16 - 111.62: 10154 111.62 - 119.09: 8083 119.09 - 126.56: 10998 126.56 - 134.03: 339 Bond angle restraints: 29822 Sorted by residual: angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA LEU D 608 " pdb=" CB LEU D 608 " pdb=" CG LEU D 608 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 ... (remaining 29817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 12994 24.39 - 48.78: 433 48.78 - 73.18: 131 73.18 - 97.57: 17 97.57 - 121.96: 6 Dihedral angle restraints: 13581 sinusoidal: 6221 harmonic: 7360 Sorted by residual: dihedral pdb=" C27 POV B 803 " pdb=" C28 POV B 803 " pdb=" C29 POV B 803 " pdb="C210 POV B 803 " ideal model delta sinusoidal sigma weight residual 127.48 -110.56 -121.96 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C27 POV A 809 " pdb=" C28 POV A 809 " pdb=" C29 POV A 809 " pdb="C210 POV A 809 " ideal model delta sinusoidal sigma weight residual 127.48 -116.73 -115.79 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C3 POV B 808 " pdb=" C31 POV B 808 " pdb=" O31 POV B 808 " pdb=" C32 POV B 808 " ideal model delta sinusoidal sigma weight residual 172.61 -76.70 -110.69 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 13578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2038 0.024 - 0.047: 729 0.047 - 0.071: 342 0.071 - 0.095: 83 0.095 - 0.119: 41 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA ILE B 734 " pdb=" N ILE B 734 " pdb=" C ILE B 734 " pdb=" CB ILE B 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 734 " pdb=" N ILE D 734 " pdb=" C ILE D 734 " pdb=" CB ILE D 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 3230 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 181 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.017 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5933 2.81 - 3.33: 21654 3.33 - 3.86: 36181 3.86 - 4.38: 44415 4.38 - 4.90: 74855 Nonbonded interactions: 183038 Sorted by model distance: nonbonded pdb=" O GLY B 638 " pdb="NA NA A 801 " model vdw 2.291 2.470 nonbonded pdb=" O GLY C 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY A 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY D 638 " pdb="NA NA A 801 " model vdw 2.293 2.470 nonbonded pdb=" NZ LYS C 589 " pdb=" O14 POV C 805 " model vdw 2.297 2.520 ... (remaining 183033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or resid 805 or (resid 806 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) selection = (chain 'B' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.950 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 55.860 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.037 22222 Z= 0.092 Angle : 0.385 7.989 29822 Z= 0.190 Chirality : 0.032 0.119 3233 Planarity : 0.002 0.030 3600 Dihedral : 13.139 121.958 8793 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2484 helix: 1.20 (0.13), residues: 1556 sheet: 3.44 (0.63), residues: 64 loop : -1.31 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 739 HIS 0.002 0.000 HIS C 301 PHE 0.004 0.001 PHE D 377 TYR 0.006 0.001 TYR D 208 ARG 0.002 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 460 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 468 average time/residue: 1.4282 time to fit residues: 753.8768 Evaluate side-chains 309 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 305 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.1137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 197 ASN A 205 ASN A 279 GLN A 346 GLN A 452 ASN A 580 GLN A 645 GLN A 647 ASN A 695 GLN B 143 GLN B 197 ASN B 279 GLN B 346 GLN B 452 ASN B 570 GLN B 580 GLN B 645 GLN B 647 ASN B 695 GLN C 143 GLN C 197 ASN C 279 GLN C 346 GLN C 452 ASN C 580 GLN C 645 GLN C 695 GLN D 143 GLN D 197 ASN D 279 GLN D 346 GLN D 452 ASN D 580 GLN D 645 GLN D 695 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 22222 Z= 0.389 Angle : 0.700 12.495 29822 Z= 0.342 Chirality : 0.043 0.158 3233 Planarity : 0.005 0.045 3600 Dihedral : 17.209 137.125 3885 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.61 % Allowed : 10.15 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2484 helix: 0.83 (0.12), residues: 1624 sheet: 2.86 (0.63), residues: 64 loop : -1.40 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 692 HIS 0.007 0.002 HIS C 301 PHE 0.016 0.002 PHE A 526 TYR 0.020 0.003 TYR A 575 ARG 0.005 0.001 ARG C 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 331 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 18 residues processed: 382 average time/residue: 1.5035 time to fit residues: 647.0765 Evaluate side-chains 294 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.2749 time to fit residues: 6.4793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 200 optimal weight: 0.0020 chunk 223 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 580 GLN A 750 ASN B 182 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 750 ASN C 220 ASN C 580 GLN C 750 ASN D 182 ASN D 580 GLN D 750 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22222 Z= 0.154 Angle : 0.509 11.332 29822 Z= 0.250 Chirality : 0.036 0.146 3233 Planarity : 0.003 0.031 3600 Dihedral : 16.455 124.392 3885 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.03 % Allowed : 14.62 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2484 helix: 1.28 (0.12), residues: 1588 sheet: 3.13 (0.61), residues: 64 loop : -1.55 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.006 0.001 HIS B 301 PHE 0.009 0.001 PHE D 506 TYR 0.016 0.002 TYR A 208 ARG 0.002 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 305 time to evaluate : 2.589 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 14 residues processed: 344 average time/residue: 1.6449 time to fit residues: 632.5161 Evaluate side-chains 300 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 286 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 3.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 580 GLN A 750 ASN B 570 GLN B 750 ASN C 182 ASN C 279 GLN C 580 GLN C 750 ASN D 580 GLN D 750 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 22222 Z= 0.314 Angle : 0.627 11.954 29822 Z= 0.305 Chirality : 0.041 0.160 3233 Planarity : 0.004 0.033 3600 Dihedral : 16.872 121.182 3885 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.75 % Allowed : 14.35 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2484 helix: 0.95 (0.12), residues: 1636 sheet: 2.97 (0.64), residues: 64 loop : -1.42 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 710 HIS 0.009 0.001 HIS D 301 PHE 0.011 0.002 PHE A 748 TYR 0.016 0.002 TYR A 208 ARG 0.003 0.001 ARG B 698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 317 time to evaluate : 2.364 Fit side-chains outliers start: 61 outliers final: 26 residues processed: 365 average time/residue: 1.5488 time to fit residues: 634.4321 Evaluate side-chains 321 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 295 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.3478 time to fit residues: 5.4302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 3 optimal weight: 0.0470 chunk 178 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 0.0970 chunk 60 optimal weight: 0.3980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 585 HIS C 750 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22222 Z= 0.141 Angle : 0.499 10.784 29822 Z= 0.245 Chirality : 0.036 0.185 3233 Planarity : 0.003 0.030 3600 Dihedral : 16.067 121.083 3885 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.53 % Allowed : 14.98 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2484 helix: 1.42 (0.12), residues: 1592 sheet: 3.13 (0.62), residues: 64 loop : -1.59 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 710 HIS 0.005 0.001 HIS D 301 PHE 0.011 0.001 PHE D 506 TYR 0.014 0.001 TYR A 208 ARG 0.001 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 307 time to evaluate : 2.508 Fit side-chains outliers start: 56 outliers final: 26 residues processed: 347 average time/residue: 1.5697 time to fit residues: 611.5510 Evaluate side-chains 312 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 286 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 1.8498 time to fit residues: 11.4371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 0.0270 chunk 47 optimal weight: 0.9980 chunk 140 optimal weight: 0.0000 chunk 59 optimal weight: 0.2980 chunk 239 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS B 750 ASN C 750 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22222 Z= 0.143 Angle : 0.500 10.638 29822 Z= 0.244 Chirality : 0.036 0.145 3233 Planarity : 0.003 0.030 3600 Dihedral : 15.776 119.638 3885 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.71 % Allowed : 15.79 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2484 helix: 1.58 (0.12), residues: 1592 sheet: 3.21 (0.62), residues: 64 loop : -1.58 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 710 HIS 0.005 0.001 HIS D 301 PHE 0.009 0.001 PHE D 316 TYR 0.013 0.001 TYR B 208 ARG 0.001 0.000 ARG D 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 302 time to evaluate : 2.401 Fit side-chains outliers start: 38 outliers final: 23 residues processed: 332 average time/residue: 1.5410 time to fit residues: 575.2003 Evaluate side-chains 309 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 3.1660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 201 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 750 ASN C 279 GLN C 750 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 750 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22222 Z= 0.166 Angle : 0.518 10.757 29822 Z= 0.253 Chirality : 0.036 0.148 3233 Planarity : 0.003 0.028 3600 Dihedral : 15.734 119.289 3885 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.26 % Allowed : 16.06 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2484 helix: 1.57 (0.12), residues: 1592 sheet: 3.17 (0.62), residues: 64 loop : -1.57 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 710 HIS 0.006 0.001 HIS D 301 PHE 0.009 0.001 PHE C 316 TYR 0.013 0.002 TYR A 208 ARG 0.001 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 299 time to evaluate : 2.492 Fit side-chains outliers start: 50 outliers final: 28 residues processed: 332 average time/residue: 1.5942 time to fit residues: 597.7592 Evaluate side-chains 315 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 287 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.4699 time to fit residues: 4.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN B 220 ASN B 279 GLN B 750 ASN C 279 GLN C 750 ASN D 220 ASN D 279 GLN D 750 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22222 Z= 0.278 Angle : 0.614 12.431 29822 Z= 0.299 Chirality : 0.040 0.152 3233 Planarity : 0.003 0.029 3600 Dihedral : 16.316 116.086 3885 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.08 % Allowed : 16.56 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2484 helix: 1.20 (0.12), residues: 1628 sheet: 2.93 (0.63), residues: 64 loop : -1.46 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 710 HIS 0.008 0.001 HIS B 301 PHE 0.009 0.002 PHE D 522 TYR 0.016 0.002 TYR D 208 ARG 0.003 0.000 ARG D 698 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.370 Fit side-chains outliers start: 46 outliers final: 30 residues processed: 341 average time/residue: 1.5817 time to fit residues: 607.1530 Evaluate side-chains 329 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 299 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 4 average time/residue: 0.7077 time to fit residues: 6.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 174 optimal weight: 0.0670 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 750 ASN C 279 GLN C 750 ASN D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22222 Z= 0.160 Angle : 0.525 11.135 29822 Z= 0.259 Chirality : 0.036 0.149 3233 Planarity : 0.003 0.032 3600 Dihedral : 15.888 120.574 3885 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.67 % Allowed : 16.83 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2484 helix: 1.47 (0.12), residues: 1592 sheet: 3.04 (0.63), residues: 64 loop : -1.62 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 710 HIS 0.005 0.001 HIS D 301 PHE 0.014 0.001 PHE D 506 TYR 0.015 0.001 TYR A 208 ARG 0.002 0.000 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 297 time to evaluate : 2.532 Fit side-chains outliers start: 37 outliers final: 29 residues processed: 326 average time/residue: 1.6139 time to fit residues: 588.7765 Evaluate side-chains 323 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 294 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 1.2766 time to fit residues: 9.1543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 750 ASN C 182 ASN C 750 ASN D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22222 Z= 0.369 Angle : 0.687 13.531 29822 Z= 0.335 Chirality : 0.044 0.185 3233 Planarity : 0.004 0.037 3600 Dihedral : 16.760 119.541 3885 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.99 % Allowed : 16.56 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2484 helix: 0.93 (0.12), residues: 1636 sheet: 2.37 (0.64), residues: 64 loop : -1.48 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 710 HIS 0.010 0.002 HIS D 301 PHE 0.015 0.002 PHE C 506 TYR 0.020 0.003 TYR A 208 ARG 0.004 0.001 ARG B 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 2.658 Fit side-chains outliers start: 44 outliers final: 26 residues processed: 342 average time/residue: 1.6383 time to fit residues: 629.0623 Evaluate side-chains 320 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.0633 time to fit residues: 5.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 202 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 750 ASN C 750 ASN D 750 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125149 restraints weight = 23135.526| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.64 r_work: 0.3279 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22222 Z= 0.170 Angle : 0.540 11.471 29822 Z= 0.267 Chirality : 0.037 0.149 3233 Planarity : 0.003 0.035 3600 Dihedral : 16.113 121.037 3885 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.40 % Allowed : 17.33 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2484 helix: 1.22 (0.12), residues: 1620 sheet: 2.74 (0.64), residues: 64 loop : -1.53 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 710 HIS 0.005 0.001 HIS B 301 PHE 0.017 0.001 PHE D 506 TYR 0.021 0.002 TYR A 208 ARG 0.002 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9515.08 seconds wall clock time: 169 minutes 53.67 seconds (10193.67 seconds total)